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- PDB-8sso: AurA bound to danusertib and inhibiting monobody Mb2 -

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Basic information

Entry
Database: PDB / ID: 8sso
TitleAurA bound to danusertib and inhibiting monobody Mb2
Components
  • Aurora kinase A
  • Mb2
KeywordsTRANSFERASE / Complex / Kinase / Monobody
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-627 / ACETATE ION / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLudewig, H. / Kim, C. / Kern, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: A biophysical framework for double-drugging kinases.
Authors: Kim, C. / Ludewig, H. / Hadzipasic, A. / Kutter, S. / Nguyen, V. / Kern, D.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
B: Mb2
D: Aurora kinase A
E: Mb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8199
Polymers85,6894
Non-polymers1,1295
Water9,656536
1
A: Aurora kinase A
B: Mb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4996
Polymers42,8452
Non-polymers6554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
MethodPISA
2
D: Aurora kinase A
E: Mb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3193
Polymers42,8452
Non-polymers4751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.619, 73.225, 179.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified kinase / Ipl1- and aurora-related kinase 1 / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase Ayk1 / Serine/threonine-protein kinase aurora-A


Mass: 32990.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein Mb2


Mass: 9853.987 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 541 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-627 / N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE / Danusertib / PHA-739358


Mass: 474.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30N6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystals of AurA in complex with Mb2 and danusertib were obtained by combining 0.5 ul of 300 uM (10 mg/mL) AurA + 315 uM (4 mg/mL) Mb2 + 1 mM danusertib with 0.5 ul of 0.1 M BIS-TRIS pH 5.5 ...Details: Crystals of AurA in complex with Mb2 and danusertib were obtained by combining 0.5 ul of 300 uM (10 mg/mL) AurA + 315 uM (4 mg/mL) Mb2 + 1 mM danusertib with 0.5 ul of 0.1 M BIS-TRIS pH 5.5 + 0.2 M Ammonium acetate + 25 percent PEG3350. Crystals were grown at 18 degC by sitting drop. Crystals were harvested and subsequently flash frozen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.97→44.19 Å / Num. obs: 59706 / % possible obs: 95.64 % / Redundancy: 9.3 % / Biso Wilson estimate: 31.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0803 / Net I/σ(I): 20.24
Reflection shellResolution: 1.97→2.044 Å / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6010 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→44.19 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 2918 4.96 %
Rwork0.1917 55890 -
obs0.1938 58808 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.21 Å2
Refinement stepCycle: LAST / Resolution: 1.97→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 82 536 6154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275843
X-RAY DIFFRACTIONf_angle_d0.56437945
X-RAY DIFFRACTIONf_chiral_restr0.0439869
X-RAY DIFFRACTIONf_plane_restr0.00481002
X-RAY DIFFRACTIONf_dihedral_angle_d5.7894808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.33441560.29312661X-RAY DIFFRACTION98.26
2.01-2.040.30841330.26792769X-RAY DIFFRACTION100
2.04-2.080.33131410.29562742X-RAY DIFFRACTION99.97
2.08-2.120.32111430.24942755X-RAY DIFFRACTION99.97
2.12-2.160.3061500.23472749X-RAY DIFFRACTION100
2.16-2.210.29211360.23452757X-RAY DIFFRACTION100
2.21-2.260.4717610.3961065X-RAY DIFFRACTION39.04
2.26-2.320.29461220.27162235X-RAY DIFFRACTION81.16
2.32-2.380.22221430.19662763X-RAY DIFFRACTION99.97
2.38-2.450.24791430.2012778X-RAY DIFFRACTION100
2.45-2.530.24711240.19512797X-RAY DIFFRACTION100
2.53-2.620.2631520.19342755X-RAY DIFFRACTION99.97
2.62-2.720.20681370.18452787X-RAY DIFFRACTION99.97
2.72-2.850.24471460.19082775X-RAY DIFFRACTION100
2.85-30.20731270.19272808X-RAY DIFFRACTION100
3-3.180.2491430.19512785X-RAY DIFFRACTION100
3.18-3.430.24591400.19582799X-RAY DIFFRACTION99.97
3.43-3.780.23781330.18452469X-RAY DIFFRACTION87.52
3.78-4.320.23441700.16592801X-RAY DIFFRACTION99.5
4.32-5.440.18931470.14872874X-RAY DIFFRACTION99.97
5.44-44.190.17091710.16862966X-RAY DIFFRACTION99.18
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.223138699270.136067789169-0.48519114321.60264525312-1.019616323751.46574559630.0521246640675-0.356713408597-0.2477991825350.1502039717450.06687282711480.1167076402640.228231492736-0.448089173236-0.0398333926910.330118301904-0.07933239020650.0194810270840.6958962111340.007159810568050.2919290304635.6862166231615.588050269527.5743373845
21.30790990791-0.1121675380070.250178565040.54438506421-0.1974460268362.470181036580.0502857297047-0.154595825525-0.0264525359490.06779017867640.01321409692140.04812021997790.207266660537-0.399169399534-0.04032953057290.1744780486120.004854996182880.01213597810260.3123212247620.0003372058447180.21580525251112.43647073519.929068934614.1702492321
32.90205715106-0.2224534039950.4243306524621.80297316145-0.2078457625362.95485475397-0.002071362843430.146057349880.02774675051360.0137692845988-0.0158683129121-0.0358374597510.08351166805260.1391423907340.01073284982890.118349906418-0.0113121738470.02287860307470.204502373478-0.007105567396980.16510687046726.900284760719.44402226824.6766662606
46.63301134488-1.11464746119-1.182251267515.577198183292.106218271518.566716256690.6465225620110.9689636366980.27754022129-0.9149678791960.3688210906810.847561733105-0.321279300297-0.443521170847-0.7857006446440.515647214721-0.167366397861-0.03344549085930.9623402593390.243817660430.473302822198-3.08949591844.5321983187144.9299776906
55.136501984881.61529851407-0.6109461874417.62849304354-0.2379722968770.07289942010890.278643110126-0.782761916236-0.1977493747170.1251366891610.06999054019950.3814235878140.739934011218-0.378689791125-0.222066625590.386375122375-0.07421931997230.03135563432730.6526607984810.1733445633560.419224289467-3.76634269624-4.9036794772860.3991058962
64.11778414892.32009988517-3.537647992414.02810737904-5.423904842517.34365421460.02627172184190.156849911840.2732212599680.101618528425-0.0254182118151-0.01307067292710.132830645380.0718184702725-0.006351901824670.307305499645-0.1116586556910.03464962528740.5785584929460.08069994911070.343381549093.739455356661.1251548948253.7354152085
71.71427471358-2.51625994089-2.536630599314.154309389744.551055295155.237289014160.305774938469-2.278691641842.604699381170.4812821001180.03026100201170.739531522883-2.1684532608-0.0462543061977-0.1749793204061.423997800420.03048324477660.491014471630.85751980039-0.2336450866271.01150744383-0.78472200143915.073819073265.0264540657
84.588701695421.95249165899-3.049630146768.7652743026-2.584058080632.707455267760.643012739842-0.4315153467430.8194420083810.406504507122-0.613482694777-0.339017175941-0.9919530020681.467404685590.01315979602260.444967021612-0.2063933932920.02810611846770.7303643894450.03576843119650.4401286598269.446572240944.7340229279456.9466063418
92.895666290651.02104329848-1.171510672554.95387787279-2.594211276779.721743311760.238113733207-0.116947084753-0.2074837419690.2534490375150.0828768235315-0.5590227540240.1493450094410.0571041012269-0.2248436549550.281514754111-0.120024050106-0.01166990292340.5705404736280.01447427309540.4097155338292.97768537166-0.22985732016861.667357159
103.928348918342.14183815406-0.4307849510463.14734026713-1.420284652165.337411592010.217899626167-0.09286205712550.8332384052950.08780002622190.3284664699460.761048022676-0.391439517612-0.303162581501-0.5973277248250.3338760402290.02003721737220.1266604638270.5350710526940.05628123741960.448353763151-0.407446352147.1822906981156.8726758168
114.544082432962.72285359477-2.273291980143.10148087356-2.923355479687.048465066240.1952246409890.07185119235210.4729501017570.05478933193960.3489068071390.545299597865-0.264423625157-0.0436994646004-0.4771796835390.283846524967-0.03924175293140.01831290001970.6542421996220.1042331306760.4148584299852.793579864616.4278264044248.9346705194
122.90097760312-1.47270196920.3866765481481.619974844521.374180442862.955507349650.039476333050.0684648635106-1.013911307380.369366869359-0.07070518493140.5493482083031.14963246208-0.1061562587910.1482051240661.42758567583-0.06360754442640.1188529270180.429143108336-0.1339216656430.5798749310630.0567107092-17.856499783918.9206871605
132.212724339850.5177760014621.05508363563.05682599171-0.08717908445471.560652484660.206068290925-0.19352450388-0.137565867073-0.121390614033-0.006753347549060.1439040378080.694344679496-0.2500706296-0.1467985290280.7962166128830.00649277427930.06748956384160.3580104946010.04371578848370.33429328153832.1216630323-10.156581703318.3989306149
141.86859989243-0.520696071293-0.2228191073282.46467936635-0.7040368786844.020701868080.013209403035-0.167815597668-0.2849960868420.0510517200768-0.1552354885920.09131900566690.7137852925440.18426582760.1185532341690.3707663221250.0152853668795-0.006943986695950.4356966889590.04200037801250.3165233079537.0060045232.4034999036533.6043614786
152.92148402112-0.6349756414720.9099911515122.82002646694-1.029636692094.563543091930.139838726013-0.3586692906780.2278734009260.365485281962-0.269858478441-0.210152889197-0.137984751440.3165914779320.1723086609290.34928559124-0.077311698923-0.0601107573430.495955776165-0.01620083184530.27020197592138.507737472811.179808034142.0995639241
162.546577745792.5019571733-0.4349805273197.935841489611.802593108172.671921869440.0687647813999-0.0445887905447-0.2830929040810.4323291578620.0136944917276-0.1388416522040.3904755401420.00213255026687-0.04721188976331.23037305668-0.161308727553-0.3679234182180.272765542119-0.1944737630971.068043898918.7570558644-20.08836973191.94036013923
176.713244738262.238542504543.025895073097.244175880083.907782332345.01779564774-0.1181720429850.832750663210.163050498691-1.086203151720.911967538711-0.09074941241.062076745820.624923114559-0.7952235670171.00255033262-0.224069497589-0.06012795107140.542431749062-0.2108388974320.6726280675615.7320987037-20.8114380066-13.9526801793
183.80791806051-1.193398104722.064291284692.243259166490.08914738553391.40784606093-1.117154002190.355490681783-0.727490127373-0.5735464814190.4553210076410.1583140257981.16022296075-0.7803437329620.3331176937690.956416721911-0.2268106507010.1776191136740.5021810356420.002684202171680.53510737586714.6477927384-11.49413046222.79402863564
191.605981014641.014099920911.098635733014.00548008612-1.144662290259.77220827201-0.187508926050.876544281738-0.508178239373-0.7527735158710.412581677202-0.7212390018180.9631722587891.24560568519-0.3376076404470.72710510105-0.1407464768710.009859022144020.629588489427-0.3127174214340.71631584850124.6166636915-14.2861943267-9.58885365801
204.19639803644-4.41330329594-1.344924517146.879606069393.902490432493.158712720480.3611835114121.25244722346-0.179421998696-1.148085625880.0998937366896-0.8294403287230.1383672763270.88336073899-0.6683380710971.03673267177-0.10440278426-0.03983051029510.823663604514-0.03714426452660.6204848961427.3503684551-13.7013740088-12.1891107239
212.75332070385-3.85075446678-1.428753568695.527733624172.906718951825.629480685240.1070166986710.759230039151-0.907914587303-1.448819474010.355295170567-0.6720387147450.5990009406610.615552092434-0.4549473301090.982796364461-0.2587567721550.05413272929290.497422870667-0.4132737513140.94105678278419.8000273311-17.5908413228-15.4805023823
224.65798644098-1.61699703282-0.3805020650612.41090021378-1.834513111352.116916013370.2581408655220.837703597523-0.384961889924-1.328866906420.218034942692-1.235277617390.511987993241.03518975439-0.4160729944310.8116925571170.0660711339670.09440489079310.640456549632-0.3567509829710.87988215475524.9607526977-17.1083617144-7.08680468432
230.560757119115-0.301655851964-0.4035634089312.61492675765-0.7293184955350.6664633052520.3092721266450.0163245721813-0.733098506720.768145730685-0.0351216407173-0.01744018389580.1342493945310.1340660639490.1283442668960.716041059839-0.09747327917-0.06748093878810.242226475817-0.1152226862950.49962929804824.1630106642-8.434356199155.78401548464
240.43699879661.127437215410.5472530537365.996856206840.123463021241.872809654310.1414058198310.19769642346-0.341684403045-0.2224499019250.0368694176168-0.9216656580280.8315301994440.189598744756-0.689744315581.0428857290.0385235639816-0.1881626316350.477335544215-0.5616152009121.07601161123.1109713367-25.9996934128-10.9763194258
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 127 through 201 )AA127 - 2011 - 75
22chain 'A' and (resid 202 through 291 )AA202 - 29176 - 158
33chain 'A' and (resid 292 through 389 )AA292 - 389159 - 256
44chain 'B' and (resid 2 through 10 )BD2 - 101 - 9
55chain 'B' and (resid 11 through 16 )BD11 - 1610 - 15
66chain 'B' and (resid 17 through 40 )BD17 - 4016 - 39
77chain 'B' and (resid 41 through 47 )BD41 - 4740 - 46
88chain 'B' and (resid 48 through 53 )BD48 - 5347 - 52
99chain 'B' and (resid 54 through 68 )BD54 - 6853 - 67
1010chain 'B' and (resid 69 through 76 )BD69 - 7668 - 75
1111chain 'B' and (resid 77 through 93 )BD77 - 9376 - 92
1212chain 'D' and (resid 127 through 145 )DF127 - 1451 - 19
1313chain 'D' and (resid 146 through 217 )DF146 - 21720 - 91
1414chain 'D' and (resid 218 through 324 )DF218 - 32492 - 187
1515chain 'D' and (resid 325 through 389 )DF325 - 389188 - 252
1616chain 'E' and (resid 4 through 9 )EG4 - 91 - 6
1717chain 'E' and (resid 10 through 24 )EG10 - 247 - 21
1818chain 'E' and (resid 25 through 32 )EG25 - 3222 - 29
1919chain 'E' and (resid 33 through 40 )EG33 - 4030 - 37
2020chain 'E' and (resid 41 through 53 )EG41 - 5338 - 47
2121chain 'E' and (resid 54 through 69 )EG54 - 6948 - 63
2222chain 'E' and (resid 70 through 77 )EG70 - 7764 - 71
2323chain 'E' and (resid 78 through 86 )EG78 - 8672 - 80
2424chain 'E' and (resid 87 through 92 )EG87 - 9281 - 86

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